791H Senior Project Proposal

Image Filtering and Enhancement of Scanning Electron Microscope Images

Nathan BrouwerAdvisor: Rich Messner

Goal

• To improve and extract information from DNA images taken by scanning transmission electron microscope (STEM)

– Accomplished with research and use of image processing algorithms

Project Evolution

• SURF (Summer Undergraduate Research Fellowship)grant

• URA (Undergraduate Research Award)

• Honors Senior Project

BackgroundDeoxyribonucleic acid (DNA)

• Back Bone– Sugar, Phosphate groups

• Nucleotide Pairs– Adenine-Thymine– Guanine-CytosineContains Genetic Information *Main Elements: Hydrogen, Carbon, Nitrogen, Oxygen, and Phosphorus *Average distance between base pairs ~.34nm

BackgroundScanning Transmission Electron Microscope

• The STEM accelerates an ionized beam of concentrated electrons onto the sample

-raster scanning• Electrons travelling through the

sample of deflected due to the positive charge of the nuclei of the atoms in the sample

• Sensitive Camera detects the received energy at the pixel

• Areas with larger nuclei appear as dark spots

Maximum Resolution .08 nm

BackgroundScanning Transmission Electron Microscope (Dark Field)

• Metal ring just past the sample

• Deflected electrons hit the ring and induce a current

• The current is proportional to the size of the local nuclei at each pixel

• Large nuclei appear of high intensity white spots

• This method increases the contrast

Historic Problems with DNA Imaging

• Resolution– In recent years STEMs have been developed with

high enough magnification (.08nm)– This problem has been theoretically solved

• Contrast– DNA consists of molecularly “light” atoms.

Electrons aren’t deflected substantially enough to be significantly noticeable

Contrast Problem

• ZSGenetics – Danvers, MA (William Glover III, CEO)– ZS has devised methods to bind larger “marker”

atoms to certain nucleotide pairs.

– Find the markers=find the base pairs

– Avg distance between pairs is .34nm

– Calculate distance between markers to know the number of pairs between markers

Project Goals

• Using a variety of image processing algorithms

– Research and Implement a variety of algorithms in MATLAB to extract data in an intelligent and focused manner

– William from ZS will be a crucial aid in interpreting images and determining successful algorithms

Possible Algorithms

• Basic Techniques– Thresholding– pseudo color mapping– Logarithmic scale stretching– Filtering

• Higher Level Methods– maximum entropy method (noise probability estimation)

Pseudo Color Space Mapping

This is a rudimentary algorithm that assigns values to colors to better able the user to visualize information

Three Phase Iterative Approach

Research and Data Collection

Evaluation and Feedback of Algorithms by ZSGenetics

Algorithms and Testing

Create Graphical User Interface for use after project

completion

Final Report and publication

1 2 3

STEM Training and Data Collection

• Travel to Harvard University to take electron microscope safety and operations training

– This is a rare opportunity to become EM trained

– Provides a more in depth knowledge base on the function and operation of the microscope

Project Timeline

We are here.

Budget

Note:URA grant has awarded $150 for budget

Supplies Paper Color Printing 2 Reams $35.98

Flash Drives 8 GB 2 $39.98

Travel Durham-Danvers 96 mi RT 2 Trips $48.00

Durham-Cambridge 138 mi RT 3 Trips $103.50

Other Expenses Photo Copies 250 $25

Total $252.46

Dell Touch Screen Computer – Cost Share with URA budget and ECE department

Significance

• Provide a segue into Graduate Research

• Publishable Material-Useful to Engineering and Biochemistry fields

• Aid medical research to discover the relationship between genomic variation and disease

Special Thanks

• Advisor: Rich Messner• UNH ECE Department• William Glover and ZSGenetics• Daniel Reynolds• Hamel Center for Undergraduate Research